The Dolphins awoke Monday morning with an ailing offense, a struggling rookie quarterback who ranks worst in the league in third-down production, a highly paid left tackle with another late-season injury, and a star defensive end who wasn’t pleased about being on the bench during much of a critical four-quarter series Sunday.

As is often the case in December around these parts, the Dolphins have issues.

Start with Long: The Dolphins fear he will miss the final four games with a triceps injury, though that isn’t official. Coach Joe Philbin refused to comment about Long’s status.

Right tackle Jonathan Martin is expected to continue filling in at left tackle – a position he played at Stanford — with Nate Garner at right tackle.

The other big talking point Monday was more second-guessing about the decision to not use Cameron Wake and Jared Odrick during the first eight plays of the Patriots’ key fourth-quarter possession when they extended their lead to 23-13 and chewed 7:18 off the clock.

The Patriots gained 50 yards on those eight plays and were already in field-goal position by the time Wake and Odrick were reinserted.

Rookies Olivier Vernon and Derrick Shelby took their place on that drive.

Philbin defended the decision, saying he “absolutely” has no regrets.

“When you play the Patriots, with the tempo they have, it is important to have guys that are fresh and ready to roll and guys that can play hard every single snap,” he said. “That was our plan throughout the game, and we stuck with it. We were rotating guys throughout the game. We believe in guys we put in the game.”

Defensive coordinator Kevin Coyle said questioning the decision “is not warranted,” and Wake and Odrick “could not have done more than what the other guys were doing on the outside. We didn’t play well, but that had nothing to do with who was in the game.

“Shelby has done a hell of a job [this season]. Shelby and Vernon on the last drive were pluses in every snap they had. It wasn’t balls attacking the edge on us. They did what we needed them to do. There were other breakdowns.”

Shelby played 23 snaps, his most all season, and Vernon 31, higher than usual. Odrick played 43 — less than usual — but that was partly because the Dolphins used linebacker Koa Misi as a defensive end a lot of the time. Wake had 58 snaps.

“With rushers and defensive linemen, there’s a different expenditure of energy,” Coyle said. “It’s all about keeping guys fresh.”

“I’m always bothered when I’m not on the field,” Wake said Sunday. “Is it realistic to play every single snap? I don’t know, but I don’t want to be off the field.”

Though the defense stumbled late, the biggest problem Sunday was not scoring enough points. Ryan Tannehill’s accuracy (13 for 29) was subpar — “not where we want to be,” Philbin said — and he misfired on two potential touchdown passes to Brian Hartline.

Asked to assess Tannehill’s play, Philbin said: “He’s making a lot of progress,” but added: “It’s difficult to win games in this league when you’re averaging 19 points a game. We’re not scoring enough points to win games consistently.

“... There are times we have to do better offensively as a whole in our passing game. Sometimes it’s the location of the ball. Sometimes it’s the depth of the route. All those things at times aren’t clean enough. Sometimes, he doesn’t get the protection to set his feet to make a clean throw.”

On the two poorly thrown passes to Hartline, Philbin said: “You’ve got to make those plays.”

Tannehill’s statistics rank below to well-below average in 10 major categories. His seven touchdowns in 210 throws is the worst ratio in the league. His 60.2 rating on third downs is also worst.

His 72.3 rating overall is tied with Brandon Weeden for fourth-worst, ahead of only Mark Sanchez, Matt Cassel and John Skelton — all three of whom were benched during a game this season for ineffective play.

Philbin said he has given no thought to playing Matt Moore in any game this season, aside from the Jets game, when he replaced Tannehill due to injury.

Philbin was then asked if he believes he has the players needed for this offense to thrive. “Absolutely,” he said. “We had some plays out there yesterday we didn’t make. We all have to do a better job. It’s hard to win a lot of games scoring 19 points a game.”